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These instructions explain how to go from raw .lsm images of organoids to morphology measurements.

How is the data organized?

The images must be organized into folders. One folder will contain images of organoids from a single perturbation imaged on a single day. The name of the folder is always wellXX_Y, where XX is 01 - 08 (to represent what well of the 8-well chamber I was imaging) and Y is the name of the perturbation (normal, 1.6uMSU668, day04, etc). These folders are called data folders and the code is built to run on one data folder at a time.

All images in a data folder are named posZZZ.lsm where ZZZ is a unique position number (001, 002, etc).

The code will make the following assumptions about the images:

• All the images in the data folder have the same order of channels (for example, the first channel is always DAPI, etc).
• There is only 1 organoid to analyze in each image. There can be more than 1 organoid in the image, but only 1 will be analyzed.

You can track the progress of each data folder through the pipeline here. Each row represents one data folder.

I also use this document to record wet lab details about each sample. Each row represents a single sample (an 8-well chamber where each well has a different perturbation).

Instructions

The organoids2 repository (this repository) and rajlabimagetools repository must be on MATLAB's path for each step.

Prepare Images

Segment Each Structure

Identify Each Cell Type

Collect All Segmentations

Measure Features